Programming language implementation

Abstract: One of the challenges in bio-computing is to enable the efficient use and inter-operation of a wide variety of rapidly-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. In our laboratory we investigates several areas, including protein-ligand docking, protein-protein docking, and complex molecular assemblies. Over the years we have developed a number of computational tools such as molecular surfaces, phenomenological potentials, various docking and visualization programs which we use in conjunction with programs developed by others. The number of programs available to compute molecular properties and/or simulate molecular interactions (e.g., molecular dynamics, conformational analysis, quantum mechanics, distance geometry, docking methods, ab-initio methods) is large and growing rapidly. Moreover, these programs come in many flavors and variations, using different force fields, search techniques, algorithmic details (e.g., continuous space vs. discrete, Cartesian vs. torsional). Each variation presents its own characteristic set of advantages and limitations. These programs also tend to evolve rapidly and are usually not written as components, making it hard to get them to work together.

Abstract: Software engineers are faced with a dilemma. They want to write general and wellstructured programs that are flexible and easy to maintain. On the other hand, generality has a price: efficiency. A specialized program solving a particular problem is often significantly faster than a general program. However, the development of specialized software is time-consuming, and is likely to exceed the production of today’s programmers. New techniques are required to solve this so-called software crisis. Partial evaluation is a program specialization technique that reconciles the benefits of generality with efficiency. This thesis presents an automatic partial evaluator for the Ansi C programming language. The content of this thesis is analysis and transformation of C programs. We develop several analyses that support the transformation of a program into its generating extension. A generating extension is a program that produces specialized programs when executed on parts of the input. The thesis contains the following main results. • We develop a generating-extension transformation, and describe specialization of the various parts of C, including pointers and structures. • We develop constraint-based inter-procedural pointer and binding-time analysis. Both analyses are specified via non-standard type inference systems, and implemented by constraint solving. • We develop a side-effect and an in-use analysis. These analyses are developed in the classical monotone data-flow analysis framework. Some intriguing similarities with constraint-based analysis are observed. • We investigate separate and incremental program analysis and transformation. Realistic programs are structured into modules, which break down inter-procedural analyses that need global information about functions. • We prove that partial evaluation at most can accomplish linear speedup, and develop an automatic speedup analysis. • We study the stronger transformation technique driving, and initiate the development of generating super-extensions. The developments in this thesis are supported by an implementation. Throughout the chapters we present empirical results.

Abstract: In this paper we consider productivity challenges for parallel programmers and explore ways that parallel language design might help improve end-user productivity. We offer a candidate list of desirable qualities for a parallel programming language, and describe how these qualities are addressed in the design of the Chapel language. In doing so, we provide an overview of Chapel's features and how they help address parallel productivity. We also survey current techniques for parallel programming and describe ways in which we consider them to fall short of our idealized productive programming model.

Abstract: Free grammars for a variety of programming languages that allow you to quickly construct a This grammar of the Ada follows the Ada 95 Reference Manual. The revised Ada Reference Manual, consisting of the international standard (ISO/IEC 8652:2012): Information Technology -Programming Languages -Ada. Multi-core, programming language, Ada, safe parallelism.